Hi,
I'm trying to cycle through the various protonation states of a Histidine
residue (HIE,HIP,HID). I have resn and the residue number stored as
'curr_state' and 'i' respectively. My first shot at a function looked
basically like this (the real function has a a doc string and some gunk to
set up curr_state and i):
cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
if curr_state == 'HIE':
cmd.alter('%s/' % i,'resn="HID"')
elif curr_state == 'HID':
cmd.alter('%s/' % i,'resn="HIP"')
elif curr_state == 'HIP':
cmd.alter('%s/' % i,'resn="HIE"')
cmd.h_add('(%s/)'%i)
cmd.sort()
After I run this, it looks like nothing has changed. I can use something
like
iterate (114/),print resn
to see that the resn has in fact changed, but the hydrogens end up right
where they were when I started.
I've tried progressively more complex things, like this:
cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
if curr_state == 'HIE':
print "Changing HIE to HID"
cmd.alter('%s/' % i,'resn="HID"')
cmd.alter('%s/ND1' % i,'formal_charge=1.0')
cmd.h_add('%s/ND1' % i)
cmd.alter('%s/NE2' % i,'formal_charge=0.0')
cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
elif curr_state == 'HID':
print "Changing HID to HIP"
cmd.alter('%s/' % i,'resn="HIP"')
cmd.alter('%s/ND1' % i,'formal_charge=1.0')
cmd.h_add('%s/ND1' % i)
cmd.alter('%s/NE2' % i,'formal_charge=1.0')
cmd.h_add('%s/NE2' % i)
cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
elif curr_state == 'HIP':
print "Changing HIP to HIE"
cmd.alter('%s/' % i,'resn="HIE"')
cmd.alter('%s/ND1' % i,'formal_charge=0.0')
cmd.alter('%s/NE2' % i,'formal_charge=1.0')
cmd.h_add('%s/NE2' % i)
cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
cmd.sort()
But I think I may just be on the wrong track. The last snippet *appears*
to work for NE2 (and not for ND1), but I think that's just because the his
was an HIE to begin with.
Any hints?
Thanks,
-michael
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
